Journal ArticleDOI
UPARSE: highly accurate OTU sequences from microbial amplicon reads
TLDR
The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% correct bases commonly reported by other methods.Abstract:
Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.read more
Citations
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Journal ArticleDOI
Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria
Albert Barberán,Kelly S. Ramirez,Jonathan W. Leff,Jonathan W. Leff,Mark A. Bradford,Diana H. Wall,Noah Fierer,Noah Fierer +7 more
TL;DR: It is demonstrated that genomic information can be used to infer microbial traits that are difficult to measure directly and build trait-based predictions of the biogeographical patterns exhibited by microbes.
Journal ArticleDOI
Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
Zhi Bo Zhao,Ji-Zheng He,Ji-Zheng He,Stefan Geisen,Li-Li Han,Jun-Tao Wang,Ju-Pei Shen,Wenxue Wei,Yun Ting Fang,Pei Pei Li,Li-Mei Zhang +10 more
TL;DR: It is suggested that protists are the most susceptible microbiome component to the application of nitrogen fertilizers, which could help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.
Journal ArticleDOI
Greatest soil microbial diversity found in micro-habitats
Elizabeth M. Bach,Ryan J. Williams,Sarah K. Hargreaves,Fan Yang,Kirsten S. Hofmockel,Kirsten S. Hofmockel +5 more
TL;DR: The results show microaggregates support highly diverse microbial communities, including several unidentified genera, and a weighted proportional whole soil diversity, which accounted for microbes found in aggregate fractions and resulted in 65% greater bacterial richness and 100% greater fungal richness over independently sampled whole soil.
Journal ArticleDOI
Biochar decreased microbial metabolic quotient and shifted community composition four years after a single incorporation in a slightly acid rice paddy from southwest China.
Jufeng Zheng,Junhui Chen,Junhui Chen,Genxing Pan,Xiaoyu Liu,Xuhui Zhang,Lianqing Li,Rongjun Bian,Kun Cheng,Zheng Jinwei +9 more
TL;DR: It is suggested that biochar amendment may increase microbial C use efficiency and reduce some microorganisms that are capable of decomposing more recalcitrant soil C, which may help stabilization of soil organic matter in paddy soil in long term.
Posted ContentDOI
UCHIME2: improved chimera prediction for amplicon sequencing
TL;DR: UCHIME2 is described, an update of the popular UCHIME chimera detection algorithm with new modes optimized for high-resolution biological sequence reconstruction (“denoising”) and other applications and that UCHIME2 achieves higher detection accuracy than previous methods.
References
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Journal ArticleDOI
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI
UCHIME improves sensitivity and speed of chimera detection
TL;DR: UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
Todd Z. DeSantis,Philip Hugenholtz,Neils Larsen,Mark Rojas,Eoin L. Brodie,Keith Keller,Thomas Huber,Daniel Dalevi,Ping Hu,Gary L. Andersen +9 more
TL;DR: A 16S rRNA gene database (http://greengenes.lbl.gov) was used to provide chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies as mentioned in this paper.
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QIIME allows analysis of high-throughput community sequencing data.
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